There are programs that will let you make your folders completely invisible but somebody could hack their way in if the program is disabled at startup.
For actual encryption (which takes more time, but nobody can access the data without actually knowing the password) take a look at cryptext (author: Nick Payne, now discontinued... you'll have to Google it) for a very fast barebones encryption program or Axcrypt (one of the most comprehensive, yet easy to use encryption utilities & under active developement)
Both these can encrypt folders recursively and both of them are free. If you have a lot of data to encrypt/decrypt everytime cryptext should be the obvious choice. If you're looking for a well-rounded, comprehensive encryption program Axcrypt wins hands down. I use both.